New: cli command 'query'
Remove: unknown trash Mod: database micro migration
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422806777e
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193e1991f4
@ -78,7 +78,7 @@ faceCentered = true
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fuseEdges = true
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checkChartBoundary = false
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[structures.flowapprox]
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[structures.flowapproximation]
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transportProperties.nu = 1e-6
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pressure.boundaryField.inlet = { type = "fixedValue", value = 1e-3 }
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@ -167,7 +167,7 @@ faceCentered = true
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fuseEdges = true
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checkChartBoundary = false
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[structures.flowapprox]
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[structures.flowapproximation]
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transportProperties.nu = 1e-6
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pressure.boundaryField.inlet = { type = "fixedValue", value = 1e-3 }
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@ -256,7 +256,7 @@ faceCentered = true
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fuseEdges = true
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checkChartBoundary = false
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[structures.flowapprox]
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[structures.flowapproximation]
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transportProperties.nu = 1e-6
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pressure.boundaryField.inlet = { type = "fixedValue", value = 1e-3 }
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@ -4,7 +4,7 @@
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import click
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import ast
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import os, shutil
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import os, sys, shutil
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import logging
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class LiteralOption(click.Option):
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@ -192,7 +192,7 @@ def compute(stage, nprocs, force, update, params, path):
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logger.info(f"Stage: { stage }")
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if stage == "all" or stage == "mesh":
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if not case.params.get("meshresult", {}).get("status") == "Done" or force:
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if not case.params.get("meshresult", {}).get("meshStatus") == "Done" or force:
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(out, err, returncode), elapsed = timer(case.computeMesh)(path)
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if out: logger.info(out)
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@ -201,7 +201,7 @@ def compute(stage, nprocs, force, update, params, path):
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case.load(type, direction, theta)
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if case.params.get("meshresult"):
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case.params["meshresult"]["calculationTime"] = elapsed
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case.params["meshresult"]["meshCalculationTime"] = elapsed
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case.update()
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if returncode:
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@ -212,7 +212,7 @@ def compute(stage, nprocs, force, update, params, path):
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logger.info("Mesh exists. Skipping ...")
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if stage == "all" or stage == "flow":
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if not case.params.get("flowresult", {}).get("status") == "Done" or force:
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if not case.params.get("flowresult", {}).get("flowStatus") == "Done" or force:
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(out, err, returncode), elapsed = timer(case.computeFlow)(path)
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if out: logger.info(out)
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@ -221,7 +221,7 @@ def compute(stage, nprocs, force, update, params, path):
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case.load(type, direction, theta)
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if case.params.get("flowresult"):
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case.params["flowresult"]["calculationTime"] = elapsed
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case.params["flowresult"]["flowCalculationTime"] = elapsed
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case.update()
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if returncode:
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@ -281,7 +281,7 @@ def kill(path, pidfile):
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SalomeManager().killall()
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@anisotropy.command(
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help = "! Not a user command"
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help = "! Internal command"
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)
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@click.argument("root")
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@click.argument("type")
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@ -392,9 +392,118 @@ def postprocessing(path, plot):
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plt.show()
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@anisotropy.command()
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@click.option(
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"-p", "--param", "params",
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metavar = "key=value",
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multiple = True,
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cls = KeyValueOption,
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help = "Select by control parameter (type, direction, theta)"
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)
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@click.option(
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"-P", "--path", "path",
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default = os.getcwd(),
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help = "Specify directory to use (instead of cwd)"
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)
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@click.option(
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"--list", "printlist",
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is_flag = True,
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help = "Print a list of avaliable fields."
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)
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@click.option(
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"--export",
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metavar = "PATH",
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help = "Export query result to CSV."
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)
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@click.argument(
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"fields",
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required = False
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)
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def query(params, path, printlist, export, fields):
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from anisotropy import env
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from anisotropy.core.database import Database, Structure
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from pandas import DataFrame
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env.update(
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LOG = os.path.join(path, "logs"),
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BUILD = os.path.join(path, "build"),
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CONFIG = os.path.join(path, "anisotropy.toml"),
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db_path = path
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)
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args = dict()
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for param in params:
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args.update(param)
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fields = [ field.strip() for field in fields.split(",") ] if fields else []
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###
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db = Database(env["db_name"], env["db_path"])
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db.setup()
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searchargs = []
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if args.get("type"):
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searchargs.append(Structure.type == args["type"])
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if args.get("direction"):
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searchargs.append(Structure.direction == str(args["direction"]))
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if args.get("theta"):
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searchargs.append(Structure.theta == args["theta"])
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result = db.search(searchargs)
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result.sort(key = lambda src: f"{ src['type'] }{ src['direction'] }{ src['theta'] }")
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df = DataFrame(result)
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df_keys = [ key for key in df.keys() ]
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if printlist:
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click.echo("Avaliable fields for query:")
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click.echo("\t{}".format("\n\t".join(df_keys)))
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return
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if not result:
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click.echo("Empty result.")
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return
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if fields:
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for field in fields:
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if field not in df_keys:
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click.echo(f"Unknown field '{ field }'. Try to use '--list' flag to see all avaliable fields.")
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return
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df = df[fields]
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if export:
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df.to_csv(export, sep = ";")
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else:
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click.echo(df.to_string())
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###
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# CLI entry
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##
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if __name__ == "__main__":
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anisotropy()
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try:
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anisotropy()
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except KeyboardInterrupt:
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click.echo("Interrupted!")
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finally:
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from anisotropy.salomepl.utils import SalomeManager
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click.echo("Exiting ...")
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if os.path.exists("anisotropy.pid"):
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os.remove("anisotropy.pid")
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SalomeManager().killall()
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sys.exit(0)
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@ -29,8 +29,8 @@ def tryUntilDone(func):
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ret = func(*args, **kwargs)
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done = True
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except OperationalError:
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pass
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except OperationalError as e:
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logger.error(e)
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return ret
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@ -110,10 +110,10 @@ class Database(object):
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if flowQuery.exists():
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params["flow"] = flowQuery.dicts().get()
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flowapproxQuery = flowQuery.get().flowapprox
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flowapproximationQuery = flowQuery.get().flowapproximations
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if flowapproxQuery.exists():
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params["flowapprox"] = flowapproxQuery.dicts().get()
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if flowapproximationQuery.exists():
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params["flowapproximation"] = flowapproximationQuery.dicts().get()
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flowresultsQuery = flowQuery.get().flowresults
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@ -173,22 +173,73 @@ class Database(object):
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)
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)
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structureID = tryUntilDone(self._updateStructure)(params["structure"], query)
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structureID = tryUntilDone(self._updateStructure)(params.get("structure", {}), query)
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meshID = tryUntilDone(self._updateMesh)(params["mesh"], query, structureID)
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meshID = tryUntilDone(self._updateMesh)(params.get("mesh", {}), query, structureID)
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for submeshParams in params.get("submesh", []):
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tryUntilDone(self._updateSubMesh)(submeshParams, query, meshID)
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tryUntilDone(self._updateMeshResult)(params.get("meshresult", {}), query, meshID)
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flowID = tryUntilDone(self._updateFlow)(params["flow"], query, structureID)
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flowID = tryUntilDone(self._updateFlow)(params.get("flow", {}), query, structureID)
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tryUntilDone(self._updateFlowApproximation)(params.get("flowapprox", {}), query, flowID)
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tryUntilDone(self._updateFlowApproximation)(params.get("flowapproximation", {}), query, flowID)
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tryUntilDone(self._updateFlowResult)(params.get("flowresult", {}), query, flowID)
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def search(self, args: list):
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result = {}
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query = (
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Structure
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.select(Structure, Mesh, SubMesh, MeshResult, Flow, FlowApproximation, FlowResult)
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.join(
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Mesh,
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JOIN.INNER,
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on = (Mesh.structure_id == Structure.structure_id)
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)
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.join(
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SubMesh,
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JOIN.INNER,
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on = (SubMesh.mesh_id == Mesh.mesh_id)
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)
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.join(
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MeshResult,
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JOIN.INNER,
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on = (MeshResult.mesh_id == Mesh.mesh_id)
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)
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.join(
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Flow,
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JOIN.INNER,
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on = (Flow.structure_id == Structure.structure_id)
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)
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.join(
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FlowApproximation,
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JOIN.INNER,
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on = (FlowApproximation.flow_id == Flow.flow_id)
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)
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.join(
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FlowResult,
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JOIN.INNER,
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on = (FlowResult.flow_id == Flow.flow_id)
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)
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)
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for arg in args:
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query = query.where(arg)
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with self.__db.atomic():
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if not self.isempty():
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result = [ entry for entry in query.dicts() ]
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else:
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logger.error("Missed Structure table")
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return result
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def _updateStructure(self, src: dict, queryMain) -> int:
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raw = deepcopy(src)
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@ -101,8 +101,7 @@ class Anisotropy(object):
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buf = toml.load(config).get("structures")
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paramsAll = []
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# TODO: custom config and merge
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for entry in buf:
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# Shortcuts
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_theta = entry["structure"]["theta"]
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@ -133,12 +132,12 @@ class Anisotropy(object):
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"mesh": mesh,
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"submesh": deepcopy(entry["submesh"]),
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"flow": deepcopy(entry["flow"]),
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"flowapprox": deepcopy(entry["flowapprox"])
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"flowapproximation": deepcopy(entry["flowapproximation"])
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}
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# For `type = fixedValue` only
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_velocity = entryNew["flowapprox"]["velocity"]["boundaryField"]["inlet"]["value"]
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entryNew["flowapprox"]["velocity"]["boundaryField"]["inlet"]["value"] = [
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_velocity = entryNew["flowapproximation"]["velocity"]["boundaryField"]["inlet"]["value"]
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entryNew["flowapproximation"]["velocity"]["boundaryField"]["inlet"]["value"] = [
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val * _velocity for val in entryNew["structure"]["direction"]
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]
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@ -380,7 +379,7 @@ class Anisotropy(object):
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foamCase = [ "0", "constant", "system" ]
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flow = self.params["flow"]
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flowapprox = self.params["flowapprox"]
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flowapproximation = self.params["flowapproximation"]
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# ISSUE: ideasUnvToFoam cannot import mesh with '-case' flag so 'os.chdir' for that
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casePath = self.getCasePath()
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@ -447,8 +446,8 @@ class Anisotropy(object):
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openfoam.renumberMesh()
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pressureBF = flowapprox["pressure"]["boundaryField"]
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velocityBF = flowapprox["velocity"]["boundaryField"]
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pressureBF = flowapproximation["pressure"]["boundaryField"]
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velocityBF = flowapproximation["velocity"]["boundaryField"]
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openfoam.foamDictionary(
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"0/p",
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@ -138,8 +138,9 @@ class MeshResult(BaseModel):
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prisms = IntegerField(null = True)
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pyramids = IntegerField(null = True)
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status = TextField(null = True, default = "Idle")
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calculationTime = TimeField(null = True)
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meshStatus = TextField(null = True, default = "Idle")
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meshCalculationTime = TimeField(null = True)
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class Flow(BaseModel):
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flow_id = AutoField()
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@ -153,17 +154,20 @@ class Flow(BaseModel):
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class FlowApproximation(BaseModel):
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flow_approximation_id = AutoField()
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flow_id = ForeignKeyField(Flow, backref = "flowapprox")
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flow_id = ForeignKeyField(Flow, backref = "flowapproximations")
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pressure = JSONField(null = True)
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velocity = JSONField(null = True)
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transportProperties = JSONField(null = True)
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class FlowResult(BaseModel):
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flowresult_id = AutoField()
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flow_id = ForeignKeyField(Flow, backref = "flowresults")
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flowRate = FloatField(null = True)
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porosity = FloatField(null = True)
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permeability = FloatField(null = True)
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status = TextField(null = True, default = "Idle")
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calculationTime = TimeField(null = True)
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flowStatus = TextField(null = True, default = "Idle")
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flowCalculationTime = TimeField(null = True)
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Binary file not shown.
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Before Width: | Height: | Size: 284 KiB |
@ -5,3 +5,21 @@ Current anisotropy database hierarchy:
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.. figure:: ../static/er-diagram.png
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:align: center
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peewee migration
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----------------
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Example of Sqlite database migration and etc:
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.. code-block:: python
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from playhouse.migrate import SqliteMigrator, migrate
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from peewee import SqliteDatabase, FloatField
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db = SqliteDatabase("anisotropy.db")
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migrator = SqliteDatabase(db)
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migrate(
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migrator.rename_column("MeshResult", "status", "meshStatus"),
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migrator.add_column("FlowResult", "porosity", FloatField(null = True))
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)
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